Update PyVista to 0.45.0 (#374)

* Change contour_labeled to contour_labels

* Change transform inplace to False

* Update geometry tutorial

* Update package versions

* Bump version

Author: eigenvivek

diffdrr/__init__.py

@@ -1 +1 @@
-__version__ = "0.5.0"
+__version__ = "0.5.1"

diffdrr/visualization.py

@@ -238,7 +238,15 @@ def drr_to_mesh(
             subject.volume.data[0].cpu().numpy().flatten(order="F") > threshold
         )
         try:
-            mesh = grid.contour_labeled(smoothing=True, progress_bar=verbose)
+            mesh = grid.contour_labels(
+                boundary_style="strict_external",
+                smoothing=True,
+                output_mesh_type="quads",
+                pad_background=True,
+                orient_faces=True,
+                simplify_output=False,
+                progress_bar=verbose,
+            )
         except AttributeError as e:
             raise AttributeError(
                 f"{e}, ensure you are using pyvista>=0.43 and vtk>=9.3"
@@ -249,7 +257,7 @@ def drr_to_mesh(
         )
 
     # Transform the mesh using the affine matrix
-    mesh = mesh.transform(subject.volume.affine.squeeze())
+    mesh = mesh.transform(subject.volume.affine.squeeze(), inplace=False)
 
     # Preprocess the mesh
     if extract_largest:
@@ -284,7 +292,15 @@ def labelmap_to_mesh(
 
     # Run SurfaceNets
     grid.point_data["values"] = subject.mask.data[0].numpy().flatten(order="F")
-    mesh = grid.contour_labeled(smoothing=True, progress_bar=verbose)
+    mesh = grid.contour_labels(
+        boundary_style="strict_external",
+        smoothing=True,
+        output_mesh_type="quads",
+        pad_background=True,
+        orient_faces=True,
+        simplify_output=False,
+        progress_bar=verbose,
+    )
     mesh.smooth_taubin(
         n_iter=100,
         feature_angle=120.0,
@@ -298,7 +314,7 @@ def labelmap_to_mesh(
     mesh.clean(inplace=True, progress_bar=verbose)
 
     # Transform the mesh using the affine matrix
-    mesh = mesh.transform(subject.mask.affine.squeeze())
+    mesh = mesh.transform(subject.mask.affine.squeeze(), inplace=False)
 
     return mesh
 

environment.yml

@@ -18,5 +18,5 @@ dependencies:
   - fastcore
   - scipy
   - tqdm
-  - pyvista
-  - vtk
+  - pyvista>=0.45.0
+  - vtk>9.4.0

notebooks/api/04_visualization.ipynb

@@ -349,7 +349,15 @@
     "            subject.volume.data[0].cpu().numpy().flatten(order=\"F\") > threshold\n",
     "        )\n",
     "        try:\n",
-    "            mesh = grid.contour_labeled(smoothing=True, progress_bar=verbose)\n",
+    "            mesh = grid.contour_labels(\n",
+    "                boundary_style=\"strict_external\",\n",
+    "                smoothing=True, \n",
+    "                output_mesh_type='quads',\n",
+    "                pad_background=True,\n",
+    "                orient_faces=True,\n",
+    "                simplify_output=False,\n",
+    "                progress_bar=verbose,\n",
+    "            )\n",
     "        except AttributeError as e:\n",
     "            raise AttributeError(\n",
     "                f\"{e}, ensure you are using pyvista>=0.43 and vtk>=9.3\"\n",
@@ -360,7 +368,7 @@
     "        )\n",
     "\n",
     "    # Transform the mesh using the affine matrix\n",
-    "    mesh = mesh.transform(subject.volume.affine.squeeze())\n",
+    "    mesh = mesh.transform(subject.volume.affine.squeeze(), inplace=False)\n",
     "\n",
     "    # Preprocess the mesh\n",
     "    if extract_largest:\n",
@@ -403,7 +411,15 @@
     "\n",
     "    # Run SurfaceNets\n",
     "    grid.point_data[\"values\"] = subject.mask.data[0].numpy().flatten(order=\"F\")\n",
-    "    mesh = grid.contour_labeled(smoothing=True, progress_bar=verbose)\n",
+    "    mesh = grid.contour_labels(\n",
+    "        boundary_style=\"strict_external\",\n",
+    "        smoothing=True, \n",
+    "        output_mesh_type='quads',\n",
+    "        pad_background=True,\n",
+    "        orient_faces=True,\n",
+    "        simplify_output=False,\n",
+    "        progress_bar=verbose,\n",
+    "    )\n",
     "    mesh.smooth_taubin(\n",
     "        n_iter=100,\n",
     "        feature_angle=120.0,\n",
@@ -417,7 +433,7 @@
     "    mesh.clean(inplace=True, progress_bar=verbose)\n",
     "\n",
     "    # Transform the mesh using the affine matrix\n",
-    "    mesh = mesh.transform(subject.mask.affine.squeeze())\n",
+    "    mesh = mesh.transform(subject.mask.affine.squeeze(), inplace=False)\n",
     "\n",
     "    return mesh"
    ]